This research analyzes the peaks-over-threshold (POT) method for designed flood estimation needed to plan river levees, spillways and water facilities. In this study, a one-parameter exponential probability distribution has been modified by including the coefficient of λ, which represents an average number of floods and enables return period calculation within the specified period of time. The study also compares results using the Log-Pearson Type III distribution of maximum annual flows and a standard exponential distribution of the selected peaks over the threshold level. The aforementioned approach represents the standard mathematical tools for river flood design, while the proposed modification of the exponential distribution highlights the estimation of flood quantiles with longer return periods (e.g., 100, 1000 and 10,000 years). Moreover, the sensitivity analysis of the threshold selection is proposed to assist in the flood design flow estimation alongside the proposed modification of the exponential probability distribution. The study was carried out at the Danube River, and the Novi Sad hydrological station (Republic of Serbia) was used for the long-term recorded period from 1876 to 2015. The results suggest that the POT method derives more reliable estimates of design floods than the traditional statistical tools for flood estimation. The results suggest the theoretical values of the water level of the 10,000 years return period is equal to 867 cm, while the Log-Pearson Type III distribution of annual maximum flows underestimated this value for 14 cm.